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Filipek J, Chalaskiewicz K, Kosmider A, Nielipinski M, Michalak A, Bednarkiewicz M, Goslawski-Zeligowski M, Prucnal F, Sekula B, Pietrzyk-Brzezinska AJ. Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators. J Struct Biol 2024; 216:108071. [PMID: 38401830 DOI: 10.1016/j.jsb.2024.108071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.
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Affiliation(s)
- Jakub Filipek
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Katarzyna Chalaskiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Aleksandra Kosmider
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maciej Nielipinski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland; Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka Michalak
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Maria Bednarkiewicz
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Mieszko Goslawski-Zeligowski
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Filip Prucnal
- Biotechnology Students Association Ferment, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-530 Lodz, Poland
| | - Bartosz Sekula
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland
| | - Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, Lodz 90-537, Poland.
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2
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Patil RS, Sharma S, Bhaskarwar AV, Nambiar S, Bhat NA, Koppolu MK, Bhukya H. TetR and OmpR family regulators in natural product biosynthesis and resistance. Proteins 2023. [PMID: 37874037 DOI: 10.1002/prot.26621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/30/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.
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Affiliation(s)
- Rachit S Patil
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Siddhant Sharma
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Aditya V Bhaskarwar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Souparnika Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Niharika A Bhat
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Mani Kanta Koppolu
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - Hussain Bhukya
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
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3
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Singh P, Kumar A, Chhabra R, Singh K, Kaur J. MSMEG_5850, a stress-induced TetR protein, involved in global transcription regulation in Mycobacterium smegmatis. Future Microbiol 2023; 18:563-580. [PMID: 37284769 DOI: 10.2217/fmb-2022-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
Aim: To decipher the role of MSMEG_5850 in the physiology of mycobacteria. Methods: MSMEG_5850 was knocked out and RNA sequencing was performed. MSMEG_5850 protein was purified from the Escherichia coli pET28a system. Electrophoretic mobility shift assay and size exclusion chromatography were used to determine the binding of MSMEG_5850 to its motif and binding stoichiometry. The effect of nutritional stress was monitored. Results: Transcriptome analysis revealed the differential expression of 148 genes in an MSMEG_5850 knockout strain. MSMEG_5850 had control over 50 genes because those genes had a binding motif upstream of their sequence. The electrophoretic mobility shift assay showed MSMEG_5850 bound to its motif as a monomer. MSMEG_5850 was upregulated under nutritional stress and promoted the survival of mycobacteria. Conclusion: The study confirms the role of MSMEG_5850 in global transcriptional regulation.
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Affiliation(s)
- Parul Singh
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
| | - Arbind Kumar
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
- Current Address: Fellow Scientist, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ravindresh Chhabra
- Department of Biochemistry, Central University of Punjab, Bathinda, 151001, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, BMS Block-1, Sector-25, Panjab University, Chandigarh, 160014, India
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4
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- *Correspondence: Riccardo Manganelli,
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Willemse D, Moodley C, Mehra S, Kaushal D. Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate. Front Microbiol 2021; 12:744800. [PMID: 34721344 PMCID: PMC8554204 DOI: 10.3389/fmicb.2021.744800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Smoking is known to be an added risk factor for tuberculosis (TB), with nearly a quarter of the TB cases attributed to cigarette smokers in the 22 countries with the highest TB burden. Many studies have indicated a link between risk of active TB and cigarette smoke. Smoking is also known to significantly decrease TB cure and treatment completion rate and increase mortality rates. Cigarette smoke contains thousands of volatile compounds including carcinogens, toxins, reactive solids, and oxidants in both particulate and gaseous phase. Yet, to date, limited studies have analyzed the impact of cigarette smoke components on Mycobacterium tuberculosis (Mtb), the causative agent of TB. Here we report the impact of cigarette smoke condensate (CSC) on survival, mutation frequency, and gene expression of Mtb in vitro. We show that exposure of virulent Mtb to cigarette smoke increases the mutation frequency of the pathogen and strongly induces the expression of the regulon controlled by SigH—a global transcriptional regulator of oxidative stress. SigH has previously been shown to be required for Mtb to respond to oxidative stress, survival, and granuloma formation in vivo. A high-SigH expression phenotype is known to be associated with greater virulence of Mtb. In patients with pulmonary TB who smoke, these changes may therefore play an important, yet unexplored, role in the treatment efficacy by potentially enhancing the virulence of tubercle bacilli.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Chivonne Moodley
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Smriti Mehra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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6
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Laws M, Jin P, Rahman KM. Efflux pumps in Mycobacterium tuberculosis and their inhibition to tackle antimicrobial resistance. Trends Microbiol 2021; 30:57-68. [PMID: 34052094 DOI: 10.1016/j.tim.2021.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
Tuberculosis (TB), an infectious disease caused by the bacterium Mycobacterium tuberculosis, was the leading cause of mortality worldwide in 2019 due to a single infectious agent. The growing threat of strains of M. tuberculosis untreatable by modern antibiotic regimens only exacerbates this problem. In response to this continued public health emergency, research into methods of potentiating currently approved antimicrobial agents against resistant strains of M. tuberculosis is an urgent priority, and a key strategy in this regard is the design of mycobacterial efflux pump inhibitors (EPIs). This review summarises the current state of knowledge surrounding drug-related efflux pumps in M. tuberculosis and presents recent updates within the field of mycobacterial EPIs with a view to aiding the design of an effective adjunct therapy to overcome efflux-mediated resistance in TB.
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Affiliation(s)
- Mark Laws
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Peiqin Jin
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Khondaker Miraz Rahman
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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7
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Hu J, Jin K, He ZG, Zhang H. Citrate lyase CitE in Mycobacterium tuberculosis contributes to mycobacterial survival under hypoxic conditions. PLoS One 2020; 15:e0230786. [PMID: 32302313 PMCID: PMC7164622 DOI: 10.1371/journal.pone.0230786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/08/2020] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis and has evolved an ability to survive in hostile host environments. M. tuberculosis is thought to utilize the rTCA cycle to sustain its latent growth during infection, but the enzymatic characteristics and physiological function for the key citrate lyase of the rTCA cycle, MtbCitE, in the important pathogen remain unclear. In this study, we investigated the function of MtbCitE based on its structural properties and sequence comparisons with other bacterial citrate lyase subunits. We showed that several amino acid residues were important for the citrate cleavage activity of MtbCitE. Strikingly, the citrate cleavage activity of MtbCitE was inhibited by ATP, indicating that energy metabolism might couple with the regulation of MtbCitE activity, which differed from other CitEs. More interestingly, deletion of citE from Mycobacterium bovis BCG decreased the mycobacterial survival rate under hypoxic conditions, whereas complementation with citE restored the phenotype to wild-type levels. Consistently, three key rTCA cycle enzymes were positively regulated under hypoxic conditions in mycobacteria. Therefore, we characterized a unique citrate lyase MtbCitE from M. tuberculosis and found that the CitE protein significantly contributed to mycobacterial survival under hypoxic conditions.
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Affiliation(s)
- Jialing Hu
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Kaixi Jin
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zheng-Guo He
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hua Zhang
- College of Life Science and Technology, National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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8
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Khemthong S, Nuonming P, Dokpikul T, Sukchawalit R, Mongkolsuk S. Regulation and function of the flavonoid-inducible efflux system, emrR-emrAB, in Agrobacterium tumefaciens C58. Appl Microbiol Biotechnol 2019; 103:5763-5780. [PMID: 31127355 DOI: 10.1007/s00253-019-09899-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 11/29/2022]
Abstract
The expression of the Agrobacterium tumefaciens emrAB operon, which encodes a membrane fusion protein and an inner membrane protein, is inducible by various flavonoids, including apigenin, genistein, luteolin, naringenin, and quercetin. Among these flavonoids, quercetin is the best inducer, followed by genistein. The emrR gene is divergently transcribed from the emrAB operon. The EmrR protein, which belongs to the TetR transcriptional regulator family, negatively regulates the expression of emrAB and of itself. Electrophoretic mobility shift assays and DNase I footprinting showed that EmrR binds directly at two EmrR-binding sites in the emrR-emrAB intergenic region and that quercetin inhibits the DNA-binding activity of EmrR. Promoter-lacZ fusion analyses and 5' rapid amplification of cDNA ends were performed to map the emrR and emrAB promoters. Compared with the wild-type strain, the emrA mutant strain exhibited similar levels of resistance to the tested antibiotics. In contrast, disruption of emrR conferred protection against nalidixic acid and novobiocin, but it rendered A. tumefaciens sensitive to tetracycline and erythromycin. The emrR mutation also destabilized the outer membrane of A. tumefaciens, resulting in increased sensitivity to SDS and low pH. These findings demonstrate that proper regulation of emrR-emrAB is required for free-living A. tumefaciens to survive in deleterious environments in which toxic compounds are present. Nonetheless, A. tumefaciens strains that lack emrR or emrA still have the ability to cause tumors when infecting Nicotiana benthamiana plants.
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Affiliation(s)
- Sasimaporn Khemthong
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Puttamas Nuonming
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Thanittra Dokpikul
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand
| | - Rojana Sukchawalit
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok, 10210, Thailand.
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand.
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand
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9
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Song N, Li Z, Cui Z, Chen L, Cui Y, Dang G, Li Z, Li H, Liu S. The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B 1. BMC Microbiol 2019; 19:104. [PMID: 31117936 PMCID: PMC6530141 DOI: 10.1186/s12866-019-1492-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Vitamin B1 (VB1) is a crucial dietary nutrient and essential cofactor for several key enzymes in the regulation of cellular and metabolic processes, and more importantly in the activation of immune system. To date, the precise role of VB1 in Mycobacterium tuberculosis remains to be fully understood. RESULTS In this study, the transcriptional and metabolic profiles of VB1-treated Mycobacterium. bovis BCG were analyzed by RNA-sequencing and LC-MS (Liquid chromatography coupled to mass spectrometry). The selection of BCG strain was based on its common physiological features shared with M. tuberculosis. The results of cell growth assays demonstrated that VB1 inhibited the BCG growth rate in vitro. Transcriptomic analysis revealed that the expression levels of genes related to fatty acid metabolism, cholesterol metabolism, glycolipid catabolism, DNA replication, protein translation, cell division and cell wall formation were significantly downregulated in M. bovis BCG treated with VB1. In addition, the metabolomics LC-MS data indicated that most of the amino acids and adenosine diphosphate (ADP) were decreased in M. bovis BCG strain after VB1 treatment. CONCLUSIONS This study provides the molecular and metabolic bases to understand the impacts of VB1 on M.bovis BCG.
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Affiliation(s)
- Ningning Song
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhaoli Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liping Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yingying Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhe Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - He Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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10
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Tsigkinopoulou A, Hawari A, Uttley M, Breitling R. Defining informative priors for ensemble modeling in systems biology. Nat Protoc 2019; 13:2643-2663. [PMID: 30353176 DOI: 10.1038/s41596-018-0056-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ensemble modeling in molecular systems biology requires the reproducible translation of kinetic parameter data into informative probability distributions (priors), as well as approaches that sample parameters from these distributions without violating the thermodynamic consistency of the overall model. Although a number of pioneering frameworks for ensemble modeling have been published, the issue of generating informative priors has not yet been addressed. Here, we present a protocol that aims to fill this gap. This protocol discusses the collection of parameter values from a diverse range of sources (literature, databases and experiments), assessment of their plausibility, and creation of log-normal probability distributions that can be used as informative priors in ensemble modeling. Furthermore, the protocol enables sampling from the generated distributions while maintaining thermodynamic consistency. Once all parameter values have been retrieved from literature and databases, the protocol can be implemented within ~5-10 min per parameter. The aim of this protocol is to facilitate the design and use of informative distributions for ensemble modeling, especially in fields such as synthetic biology and systems medicine.
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Affiliation(s)
- Areti Tsigkinopoulou
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Aliah Hawari
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Megan Uttley
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, United Kingdom.
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11
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Machado D, Lecorche E, Mougari F, Cambau E, Viveiros M. Insights on Mycobacterium leprae Efflux Pumps and Their Implications in Drug Resistance and Virulence. Front Microbiol 2018; 9:3072. [PMID: 30619157 PMCID: PMC6300501 DOI: 10.3389/fmicb.2018.03072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/28/2018] [Indexed: 11/20/2022] Open
Abstract
Drug resistance in Mycobacterium leprae is assumed to be due to genetic alterations in the drug targets and reduced cell wall permeability. However, as observed in Mycobacterium tuberculosis, drug resistance may also result from the overactivity of efflux systems, which is mostly unexplored. In this perspective, we discuss known efflux pumps involved in M. tuberculosis drug resistance and virulence and investigate similar regions in the genome of M. leprae. In silico analysis reveals that the major M. tuberculosis efflux pumps known to be associated with drug resistance and virulence have been retained during the reductive evolutionary process that M. leprae underwent, e.g., RND superfamily, the ABC transporter BacA, and the MFS P55. However, some are absent (DinF, MATE) while others are derepressed (Mmr, SMR) in M. leprae reflecting the specific environment where M. leprae may live. The occurrence of several multidrug resistance efflux transporters shared between M. leprae and M. tuberculosis reveals potential implications in drug resistance and virulence. The conservation of the described efflux systems in M. leprae upon genome reduction indicates that these systems are potentially required for its intracellular survival and lifestyle. They potentially are involved in M. leprae drug resistance, which could hamper leprosy treatment success. Studying M. leprae efflux pumps as new drug targets is useful for future leprosy therapeutics, enhancing the global efforts to eradicate endemic leprosy, and prevent the emergence of drug resistance in afflicted countries.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Study Group for Mycobacterial Infections (ESGMYC), European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Basel, Switzerland
| | - Emmanuel Lecorche
- Université Paris Diderot, INSERM IAME UMR1137, Sorbonne Paris Cité, Paris, France.,APHP, Groupe Hospitalier Lariboisière Fernand-Widal, Laboratoire de Bacteriologie, Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Faiza Mougari
- Université Paris Diderot, INSERM IAME UMR1137, Sorbonne Paris Cité, Paris, France.,APHP, Groupe Hospitalier Lariboisière Fernand-Widal, Laboratoire de Bacteriologie, Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Emmanuelle Cambau
- Study Group for Mycobacterial Infections (ESGMYC), European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Basel, Switzerland.,Université Paris Diderot, INSERM IAME UMR1137, Sorbonne Paris Cité, Paris, France.,APHP, Groupe Hospitalier Lariboisière Fernand-Widal, Laboratoire de Bacteriologie, Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.,Study Group for Mycobacterial Infections (ESGMYC), European Society for Clinical Microbiology and Infectious Diseases (ESCMID), Basel, Switzerland
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12
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Zhu C, Liu Y, Hu L, Yang M, He ZG. Molecular mechanism of the synergistic activity of ethambutol and isoniazid against Mycobacterium tuberculosis. J Biol Chem 2018; 293:16741-16750. [PMID: 30185616 DOI: 10.1074/jbc.ra118.002693] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/26/2018] [Indexed: 11/06/2022] Open
Abstract
Isoniazid (INH) and ethambutol (EMB) are two major first-line drugs for managing tuberculosis (TB), caused by the microbe Mycobacterium tuberculosis Although co-use of these two drugs is common in clinical practice, the mechanism for the potential synergistic interplay between them remains unclear. Here, we present first evidence that INH and EMB act synergistically through a transcriptional repressor of the inhA gene, the target gene of INH encoding an enoyl-acyl carrier protein reductase of the fatty acid synthase type II system required for bacterial cell wall integrity. We report that EMB binds a hypothetical transcription factor encoded by the Rv0273c gene, designated here as EtbR. Using DNA footprinting, we found that EtbR specifically recognizes a motif sequence in the upstream region of the inhA gene. Using isothermal titration calorimetry and surface plasmon resonance assays, we observed that EMB binds EtbR in a 1:1 ratio and thereby stimulates its DNA-binding activity. When a nonlethal dose of EMB was delivered in combination with INH, EMB increased the INH susceptibility of cultured M. tuberculosis cells. In summary, EMB induces EtbR-mediated repression of inhA and thereby enhances the mycobactericidal effect of INH. Our findings uncover a molecular mechanism for the synergistic activity of two important anti-TB drugs.
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Affiliation(s)
- Chen Zhu
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu Liu
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihua Hu
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Yang
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Guo He
- From the National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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13
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Bockman MR, Engelhart CA, Dawadi S, Larson P, Tiwari D, Ferguson DM, Schnappinger D, Aldrich CC. Avoiding Antibiotic Inactivation in Mycobacterium tuberculosis by Rv3406 through Strategic Nucleoside Modification. ACS Infect Dis 2018; 4:1102-1113. [PMID: 29663798 DOI: 10.1021/acsinfecdis.8b00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
5'-[ N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine (Bio-AMS, 1) possesses selective activity against Mycobacterium tuberculosis ( Mtb) and arrests fatty acid and lipid biosynthesis through inhibition of the Mycobacterium tuberculosis biotin protein ligase ( MtBPL). Mtb develops spontaneous resistance to 1 with a frequency of at least 1 × 10-7 by overexpression of Rv3406, a type II sulfatase that enzymatically inactivates 1. In an effort to circumvent this resistance mechanism, we describe herein strategic modification of the nucleoside at the 5'-position to prevent enzymatic inactivation. The new analogues retained subnanomolar potency to MtBPL ( KD = 0.66-0.97 nM), and 5' R- C-methyl derivative 6 exhibited identical antimycobacterial activity toward: Mtb H37Rv, MtBPL overexpression, and an isogenic Rv3406 overexpression strain (minimum inhibitory concentration, MIC = 1.56 μM). Moreover, 6 was not metabolized by recombinant Rv3406 and resistant mutants to 6 could not be isolated (frequency of resistance <1.4 × 10-10) demonstrating it successfully overcame Rv3406-mediated resistance.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Peter Larson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - David M. Ferguson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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14
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Nuonming P, Khemthong S, Dokpikul T, Sukchawalit R, Mongkolsuk S. Characterization and regulation of AcrABR, a RND-type multidrug efflux system, in Agrobacterium tumefaciens C58. Microbiol Res 2018; 214:146-155. [PMID: 30031477 DOI: 10.1016/j.micres.2018.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/11/2018] [Accepted: 06/30/2018] [Indexed: 10/28/2022]
Abstract
Agrobacterium tumefaciens AcrR is the transcriptional repressor of the acrABR operon. The AcrAB efflux pump confers resistance to various toxic compounds, including antibiotics [ciprofloxacin (CIP), nalidixic acid (NAL), novobiocin (NOV) and tetracycline (TET)], a detergent [sodium dodecyl sulfate (SDS)] and a biocide [triclosan (TRI)]. The sequence to which AcrR specifically binds in the acrA promoter region was determined by EMSA and DNase I footprinting. The AcrR-DNA interaction was abolished by adding NAL, SDS and TRI. Quantitative real time-PCR analysis showed that induction of the acrA transcript occurred when wild-type cells were exposed to NAL, SDS and TRI. Indole is a signaling molecule that increases the antibiotic resistance of bacteria, at least in part, through activation of efflux pumps. Expression of the A. tumefaciens acrA transcript was also inducible by indole in a dose-dependent manner. Indole induced protection against CIP, NAL and SDS but enhanced susceptibility to NOV and TRI. Additionally, the TET resistance of A. tumefaciens was not apparently modulated by indole. A. tumefaciens AcrAB played a dominant role and was required for tolerance to high levels of the toxic compounds. Understanding the regulation of multidrug efflux pumps and bacterial adaptive responses to intracellular and extracellular signaling molecules for antibiotic resistance is essential. This information will be useful for the rational design of effective treatments for bacterial infection to overcome possible multidrug-resistant pathogens.
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Affiliation(s)
- Puttamas Nuonming
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Sasimaporn Khemthong
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Thanittra Dokpikul
- Environmental Toxicology, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand
| | - Rojana Sukchawalit
- Applied Biological Sciences, Chulabhorn Graduate Institute, Lak Si, Bangkok 10210, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand.
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Lak Si, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Ministry of Education, Bangkok, Thailand; Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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15
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Yan L, Tang Q, Guan Z, Pei K, Zou T, He J. Structural insights into operator recognition by BioQ in the Mycobacterium smegmatis biotin synthesis pathway. Biochim Biophys Acta Gen Subj 2018; 1862:1843-1851. [PMID: 29852200 DOI: 10.1016/j.bbagen.2018.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/18/2018] [Accepted: 05/19/2018] [Indexed: 10/14/2022]
Abstract
BACKGROUND Biotin is an essential cofactor in living organisms. The TetR family transcriptional regulator (TFTR) BioQ is the main regulator of biotin synthesis in Mycobacterium smegmatis. BioQ represses the expression of its target genes by binding to a conserved palindromic DNA sequence (the BioQ operator). However, the mechanism by which BioQ recognizes this DNA element has not yet been fully elucidated. METHODS/RESULTS We solved the crystal structures of the BioQ homodimer in its apo-form and in complex with its specific operator at 2.26 Å and 2.69 Å resolution, respectively. BioQ inserts the N-terminal recognition helix of each protomer into the corresponding major grooves of its operator and stabilizes the formation of the complex via electrostatic interactions and hydrogen bonding to induce conformational changes in both the DNA and BioQ. The DNA interface of BioQ is rich in positively charged residues, which help BioQ stabilize DNA binding. We elucidated the structural basis of DNA recognition by BioQ for the first time and identified the amino acid residues responsible for DNA binding via further site-directed mutagenesis. GENERAL SIGNIFICANCE Our findings clearly elucidate the mechanism by which BioQ recognizes its operator in the biotin synthesis pathway and reveal the unique structural characteristics of BioQ that are distinct from other TFTR members.
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Affiliation(s)
- Ling Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qing Tang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zeyuan Guan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Kai Pei
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Tingting Zou
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jin He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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16
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Mu WL, Wang M, Li HJ, Huang DM, Zhang YY, Li CY, Liu Y, Wu YC. Palladium-Catalyzed Regioselective Oxidative Annulation of Cyclohexanones and 2-Aminophenyl Ketones Using Molecular Oxygen as the Sole Oxidant. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700715] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wan-Lu Mu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Meirong Wang
- School of Materials Science and Engineering; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Hui-Jing Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Deng-Ming Huang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yi-Yun Zhang
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Chao-Yi Li
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Ying Liu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
| | - Yan-Chao Wu
- School of Marine Science and Technology; Harbin Institute of Technology; Weihai 264209 People's Republic of China
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry Chinese Academy of Sciences; Beijing 100190 People's Republic of China
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17
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18
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Bhukya H, Jana AK, Sengupta N, Anand R. Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence. J Struct Biol 2017; 198:134-146. [PMID: 28343010 DOI: 10.1016/j.jsb.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/13/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3.95Å. Furthermore, to refine and compliment the results, atomistic molecular dynamics simulations were carried out using the X-ray structure as the template. The studies reveal that CprB binds to DNA as dimer of dimers with this mode of interaction results in minimal distortion in the DNA, enabling these proteins to recognize multiple sequences with varying affinity. Another crucial finding from our simulation results was that the positively charged N-terminal arm of CprB brings extra stability to the protein-DNA complex by interacting with the minor-groove of the DNA and anchoring itself to the phosphate backbone. Corroborating electrophoretic mobility shift assay and fluorescence anisotropy experiments showed that the mutant ΔN6-CprB exhibited about 7-8 fold reduced DNA binding. Comparison with other TetR-FTRs reveals that this strategy is also employed by over 25% of TetR-FTRs, where N-terminal anchoring mechanism is used to enhance selectivity for a particular DNA sequence.
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Affiliation(s)
- Hussain Bhukya
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; IITB-Monash Research Academy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asis K Jana
- India Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Neelanjana Sengupta
- Dept. of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, W. Bengal, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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19
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Hernando-Amado S, Blanco P, Alcalde-Rico M, Corona F, Reales-Calderón JA, Sánchez MB, Martínez JL. Multidrug efflux pumps as main players in intrinsic and acquired resistance to antimicrobials. Drug Resist Updat 2016; 28:13-27. [PMID: 27620952 DOI: 10.1016/j.drup.2016.06.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/31/2016] [Accepted: 06/23/2016] [Indexed: 12/31/2022]
Abstract
Multidrug efflux pumps constitute a group of transporters that are ubiquitously found in any organism. In addition to other functions with relevance for the cell physiology, efflux pumps contribute to the resistance to compounds used for treating different diseases, including resistance to anticancer drugs, antibiotics or antifungal compounds. In the case of antimicrobials, efflux pumps are major players in both intrinsic and acquired resistance to drugs currently in use for the treatment of infectious diseases. One important aspect not fully explored of efflux pumps consists on the identification of effectors able to induce their expression. Indeed, whereas the analysis of clinical isolates have shown that mutants overexpressing these resistance elements are frequently found, less is known on the conditions that may trigger expression of efflux pumps, hence leading to transient induction of resistance in vivo, a situation that is barely detectable using classical susceptibility tests. In the current article we review the structure and mechanisms of regulation of the expression of bacterial and fungal efflux pumps, with a particular focus in those for which a role in clinically relevant resistance has been reported.
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Affiliation(s)
- Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Paula Blanco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Jose A Reales-Calderón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - María B Sánchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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20
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Honeyborne I, McHugh TD, Kuittinen I, Cichonska A, Evangelopoulos D, Ronacher K, van Helden PD, Gillespie SH, Fernandez-Reyes D, Walzl G, Rousu J, Butcher PD, Waddell SJ. Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy. BMC Med 2016; 14:68. [PMID: 27055815 PMCID: PMC4825072 DOI: 10.1186/s12916-016-0609-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/23/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND New treatment options are needed to maintain and improve therapy for tuberculosis, which caused the death of 1.5 million people in 2013 despite potential for an 86 % treatment success rate. A greater understanding of Mycobacterium tuberculosis (M.tb) bacilli that persist through drug therapy will aid drug development programs. Predictive biomarkers for treatment efficacy are also a research priority. METHODS AND RESULTS Genome-wide transcriptional profiling was used to map the mRNA signatures of M.tb from the sputa of 15 patients before and 3, 7 and 14 days after the start of standard regimen drug treatment. The mRNA profiles of bacilli through the first 2 weeks of therapy reflected drug activity at 3 days with transcriptional signatures at days 7 and 14 consistent with reduced M.tb metabolic activity similar to the profile of pre-chemotherapy bacilli. These results suggest that a pre-existing drug-tolerant M.tb population dominates sputum before and after early drug treatment, and that the mRNA signature at day 3 marks the killing of a drug-sensitive sub-population of bacilli. Modelling patient indices of disease severity with bacterial gene expression patterns demonstrated that both microbiological and clinical parameters were reflected in the divergent M.tb responses and provided evidence that factors such as bacterial load and disease pathology influence the host-pathogen interplay and the phenotypic state of bacilli. Transcriptional signatures were also defined that predicted measures of early treatment success (rate of decline in bacterial load over 3 days, TB test positivity at 2 months, and bacterial load at 2 months). CONCLUSIONS This study defines the transcriptional signature of M.tb bacilli that have been expectorated in sputum after two weeks of drug therapy, characterizing the phenotypic state of bacilli that persist through treatment. We demonstrate that variability in clinical manifestations of disease are detectable in bacterial sputa signatures, and that the changing M.tb mRNA profiles 0-2 weeks into chemotherapy predict the efficacy of treatment 6 weeks later. These observations advocate assaying dynamic bacterial phenotypes through drug therapy as biomarkers for treatment success.
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Affiliation(s)
- Isobella Honeyborne
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, NW3 2PF, UK
| | - Iitu Kuittinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
| | - Anna Cichonska
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Katharina Ronacher
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Paul D van Helden
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Stephen H Gillespie
- Medical and Biological Sciences Building, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9TF, UK
| | - Delmiro Fernandez-Reyes
- Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Paediatrics, University College Hospital, College of Medicine of the University of Ibadan, Ibadan, Nigeria
| | - Gerhard Walzl
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research and Medical Research Council Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Western Cape, South Africa
| | - Juho Rousu
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
| | - Philip D Butcher
- Institute for Infection and Immunity, St George's University of London, London, SW17 0RE, UK
| | - Simon J Waddell
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK.
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21
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Wu W, Sun X, Gao Y, Jiang J, Cui Z, Ge B, Wu H, Zhang L, Li Y. Genome-Wide De Novo Prediction of Cis-Regulatory Binding Sites in Mycobacterium tuberculosis H37Rv. PLoS One 2016; 11:e0148965. [PMID: 26886880 PMCID: PMC4757040 DOI: 10.1371/journal.pone.0148965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 01/26/2016] [Indexed: 12/03/2022] Open
Abstract
The transcription regulatory system of Mycobacterium tuberculosis (M. tb) remains incompletely understood. In this study, we have applied the eGLECLUBS algorithm to a group of related prokaryotic genomes for de novo genome-wide prediction of cis-regulatory binding sites (CRBSs) in M. tb H37Rv. The top 250 clusters from our prediction recovered 83.3% (50/60) of all known CRBSs in extracted inter-operonic sequences of this strain. We further demonstrated that the integration of our prediction results with the ChIP-Seq datasets is very effective in identifying true binding sites of TFs. Using electrophoretic mobility shift assays and real-time RT-PCR, we experimentally verified our prediction of CRBSs for Rv0081, an important transcription factor thought to be involved in regulation of M. tb under hypoxia.
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Affiliation(s)
- Wei Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Xian Sun
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Yun Gao
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Jun Jiang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Zhenling Cui
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School, Tongji University, Shanghai, China
| | - Hai Wu
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
| | - Lu Zhang
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
- * E-mail: ;
| | - Yao Li
- State Key Lab of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, College of Life Sciences, Fudan University, Shanghai, PR China
- * E-mail: ;
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22
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Mahendar L, Satyanarayana G. Copper catalyzed coupling of protecting group free and sterically hindered 2-bromobenzyl tertiary alcohols with phenols and anilines: facile synthesis of xanthenes and dihydroacridines. RSC Adv 2016. [DOI: 10.1039/c6ra03447k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Protecting group free and sterically hindered tertiary alcohols used in coupling reaction. Two-step process with a single column chromatography. Synthesis of interesting xanthenes and dihydroacridines.
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Affiliation(s)
- Lodi Mahendar
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
| | - Gedu Satyanarayana
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy
- India
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23
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Hu J, Zhao L, Yang M. A GntR family transcription factor positively regulates mycobacterial isoniazid resistance by controlling the expression of a putative permease. BMC Microbiol 2015; 15:214. [PMID: 26474554 PMCID: PMC4609117 DOI: 10.1186/s12866-015-0556-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/08/2015] [Indexed: 01/13/2023] Open
Abstract
Background Bacteria use transcriptional regulation to respond to environmental stresses. Specifically, exposure to antibacterial drugs is deemed to be an atypical stress, and altering transcriptional regulation in response to such stress can increase bacterial drug resistance. However, only a few transcription factors that regulate drug resistance have been reported. Results In the present study, a GntR family transcription factor, encoded by the MSMEG_0535 (Ms0535) gene, was shown to be an isoniazid (INH) resistance regulator in Mycobacterium smegmatis. When the Ms0535 gene was overexpressed, cells showed a significant increase in INH resistance. First, the interaction between Ms0535 and its own promoter was determined, and a conserved 26-bp palindromic DNA binding motif was identified using electrophoretic mobility shift and DNaseI footprinting assays. Second, quantitative reverse transcription-PCR assays showed that Ms0535 acted as a transcriptional activator, and positively regulated its own expression, as well as that of a permease encoded by the MSMEG_0534 (Ms0534) gene. Similar to the case for the Ms0535 gene, a recombinant Ms0534-overexpressing strain also exhibited increased INH resistance compared with the wild-type strain. Furthermore, we showed that Ms0535 and Ms0534 deletion strains were more sensitive to INH than the wild-type strain. Interestingly, overexpressing Ms0534 in the Ms0535 deletion strain enhanced its INH resistance. In contrast, the Ms0534 deletion strain was still sensitive to INH even when Ms0535 was overexpressed. These findings suggest that Ms0534 is an effector protein that affects INH resistance in M. smegmatis. Conclusions In summary, the GntR transcriptional regulator Ms0535 positively regulates INH resistance by transcriptionally regulating the expression of the Ms0534 permease in M. smegmatis. These results improve our understanding of the role of transcriptional regulation in INH drug resistance in mycobacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0556-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jialing Hu
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lei Zhao
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Min Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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24
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Chou TH, Delmar JA, Wright CC, Kumar N, Radhakrishnan A, Doh JK, Licon MH, Bolla JR, Lei HT, Rajashankar KR, Su CC, Purdy GE, Yu EW. Crystal structure of the Mycobacterium tuberculosis transcriptional regulator Rv0302. Protein Sci 2015; 24:1942-55. [PMID: 26362239 DOI: 10.1002/pro.2802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/08/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis is a pathogenic bacterial species, which is neither Gram positive nor Gram negative. It has a unique cell wall, making it difficult to kill and conferring resistance to antibiotics that disrupt cell wall biosynthesis. Thus, the mycobacterial cell wall is critical to the virulence of these pathogens. Recent work shows that the mycobacterial membrane protein large (MmpL) family of transporters contributes to cell wall biosynthesis by exporting fatty acids and lipidic elements of the cell wall. The expression of the Mycobacterium tuberculosis MmpL proteins is controlled by a complicated regulatory network system. Here we report crystallographic structures of two forms of the TetR-family transcriptional regulator Rv0302, which participates in regulating the expression of MmpL proteins. The structures reveal a dimeric, two-domain molecule with architecture consistent with the TetR family of regulators. Comparison of the two Rv0302 crystal structures suggests that the conformational changes leading to derepression may be due to a rigid body rotational motion within the dimer interface of the regulator. Using fluorescence polarization and electrophoretic mobility shift assays, we demonstrate the recognition of promoter and intragenic regions of multiple mmpL genes by this protein. In addition, our isothermal titration calorimetry and electrophoretic mobility shift experiments indicate that fatty acids may be the natural ligand of this regulator. Taken together, these experiments provide new perspectives on the regulation of the MmpL family of transporters.
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Affiliation(s)
- Tsung-Han Chou
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Jared A Delmar
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Catherine C Wright
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, 97239
| | - Nitin Kumar
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
| | | | - Julia K Doh
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, 97239
| | - Meredith H Licon
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, 97239
| | - Jani Reddy Bolla
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
| | - Hsiang-Ting Lei
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
| | - Kanagalaghatta R Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Argonne National Laboratory, Cornell University, Argonne, Illinois, 60439
| | - Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Georgiana E Purdy
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon, 97239
| | - Edward W Yu
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011.,Department of Chemistry, Iowa State University, Ames, Iowa, 50011
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25
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Delmar JA, Chou TH, Wright CC, Licon MH, Doh JK, Radhakrishnan A, Kumar N, Lei HT, Bolla JR, Rajashankar KR, Su CC, Purdy GE, Yu EW. Structural Basis for the Regulation of the MmpL Transporters of Mycobacterium tuberculosis. J Biol Chem 2015; 290:28559-28574. [PMID: 26396194 DOI: 10.1074/jbc.m115.683797] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Indexed: 11/06/2022] Open
Abstract
The mycobacterial cell wall is critical to the virulence of these pathogens. Recent work shows that the MmpL (mycobacterial membrane protein large) family of transporters contributes to cell wall biosynthesis by exporting fatty acids and lipidic elements of the cell wall. The expression of the Mycobacterium tuberculosis MmpL proteins is controlled by a complex regulatory network, including the TetR family transcriptional regulators Rv3249c and Rv1816. Here we report the crystal structures of these two regulators, revealing dimeric, two-domain molecules with architecture consistent with the TetR family of regulators. Buried extensively within the C-terminal regulatory domains of Rv3249c and Rv1816, we found fortuitous bound ligands, which were identified as palmitic acid (a fatty acid) and isopropyl laurate (a fatty acid ester), respectively. Our results suggest that fatty acids may be the natural ligands of these regulatory proteins. Using fluorescence polarization and electrophoretic mobility shift assays, we demonstrate the recognition of promoter and intragenic regions of multiple mmpL genes by these proteins. Binding of palmitic acid renders these regulators incapable of interacting with their respective operator DNAs, which will result in derepression of the corresponding mmpL genes. Taken together, these experiments provide new perspectives on the regulation of the MmpL family of transporters.
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Affiliation(s)
- Jared A Delmar
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Tsung-Han Chou
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Catherine C Wright
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Meredith H Licon
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Julia K Doh
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | | | - Nitin Kumar
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Hsiang-Ting Lei
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Jani Reddy Bolla
- Departments of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Kanagalaghatta R Rajashankar
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439
| | - Chih-Chia Su
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Georgiana E Purdy
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239
| | - Edward W Yu
- Departments of Physics and Astronomy, Iowa State University, Ames, Iowa 50011; Departments of Chemistry, Iowa State University, Ames, Iowa 50011.
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26
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Yang M, Gao CH, Hu J, Zhao L, Huang Q, He ZG. InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG. Sci Rep 2015; 5:13969. [PMID: 26353937 PMCID: PMC4564863 DOI: 10.1038/srep13969] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/12/2015] [Indexed: 02/03/2023] Open
Abstract
Isoniazid (INH), an anti-tuberculosis (TB) drug, has been widely used for nearly 60 years. However, the pathway through which Mycobacterium tuberculosis responds INH remain largely unclear. In this study, we characterized a novel transcriptional factor, InbR, which is encoded by Rv0275c and belongs to the TetR family, that is directly responsive to INH. Disrupting inbR made mycobacteria more sensitive to INH, whereas overexpressing inbR decreased bacterial susceptibility to the drug. InbR could bind specifically to the upstream region of its own operon at two inverted repeats and act as an auto-repressor. Furthermore, InbR directly bind with INH, and the binding reduced InbR’s DNA-binding ability. Interestingly, susceptibilities were also changed by InbR for other anti-TB drugs, such as rifampin, implying that InbR may play a role in multi-drug resistance. Additionally, microarray analyses revealed a portion genes of the inbR regulon have similar expression patterns in inbR-overexpressing strain and INH-treated wild type strain, suggesting that these genes, for example iniBAC, may be responsible to the drug resistance of inbR-overexpressing strain. The regulation of these genes by InbR were further assessed by ChIP-seq assay. InbR may regulate multiple drug resistance of mycobacteria through the regulation of these genes.
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Affiliation(s)
- Min Yang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chun-Hui Gao
- School of Life Sciences and CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jialing Hu
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Zhao
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng-Guo He
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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27
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Balhana RJC, Singla A, Sikder MH, Withers M, Kendall SL. Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions. BMC Genomics 2015; 16:479. [PMID: 26115658 PMCID: PMC4482099 DOI: 10.1186/s12864-015-1696-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 06/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria. RESULTS We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs. CONCLUSION This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown.
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Affiliation(s)
- Ricardo J C Balhana
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK. .,Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Stag Hill, Guildford, GU2 7XH, UK.
| | - Ashima Singla
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK. .,Indian Institute of Technology Kanpur, Kanpur, India.
| | - Mahmudul Hasan Sikder
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK. .,Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
| | - Mike Withers
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK.
| | - Sharon L Kendall
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Royal College street, Camden, London, NW1 OTU, UK.
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28
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Wang TJ, Chen WW, Li Y, Xu MH. Facile synthesis of acridines via Pd(0)-diphosphine complex-catalyzed tandem coupling/cyclization protocol. Org Biomol Chem 2015; 13:6580-6. [PMID: 25982344 DOI: 10.1039/c5ob00755k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile and efficient approach for the synthesis of a variety of acridines via the tandem coupling/cyclization of substituted 2-bromobenzaldehydes and anilines is described. The reaction can be accomplished with ease in the presence of a catalytic amount of Pd2(dba)3 and diphosphine ligand dppf, providing a broad range of substituted acridines in good to excellent yields (up to 99%). The Lewis acid, AlCl3, is required to promote the cyclization for less electron-rich anilines.
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Affiliation(s)
- Ting-Jun Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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29
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Jiang J, Gu J, Zhang L, Zhang C, Deng X, Dou T, Zhao G, Zhou Y. Comparing Mycobacterium tuberculosis genomes using genome topology networks. BMC Genomics 2015; 16:85. [PMID: 25766780 PMCID: PMC4342819 DOI: 10.1186/s12864-015-1259-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 01/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. Results In this work, we introduce a ‘Genome Topology Network’ (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of ‘unfixed ortholog’ has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). Conclusions The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/, and allows re-annotating the ‘lost’ genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes were found to be affected by SVs in M. tuberculosis genomes. We believe that the GTN method will be suitable for the exploration of genomic SVs in connection with biological features of bacterial strains, and that GTN-based phylogenetic analysis will provide additional insights into whole genome-based phylogenetic analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1259-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianping Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Jianlei Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Liang Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Chenyi Zhang
- School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, QLD 4072, Australia.
| | - Xiao Deng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, People's Republic of China.
| | - Tonghai Dou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China.
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
| | - Yan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People's Republic of China. .,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China.
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30
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Crowe AM, Stogios PJ, Casabon I, Evdokimova E, Savchenko A, Eltis LD. Structural and functional characterization of a ketosteroid transcriptional regulator of Mycobacterium tuberculosis. J Biol Chem 2014; 290:872-82. [PMID: 25406313 DOI: 10.1074/jbc.m114.607481] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catabolism of host cholesterol is critical to the virulence of Mycobacterium tuberculosis and is a potential target for novel therapeutics. KstR2, a TetR family repressor (TFR), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-H-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (HIP). Binding of KstR2 to its operator sequences is relieved upon binding of HIP-CoA. A 1.6-Å resolution crystal structure of the KstR2(Mtb)·HIP-CoA complex reveals that the KstR2(Mtb) dimer accommodates two molecules of HIP-CoA. Each ligand binds in an elongated cleft spanning the dimerization interface such that the HIP and CoA moieties interact with different KstR2(Mtb) protomers. In isothermal titration calorimetry studies, the dimer bound 2 eq of HIP-CoA with high affinity (K(d) = 80 ± 10 nm) but bound neither HIP nor CoASH. Substitution of Arg-162 or Trp-166, residues that interact, respectively, with the diphosphate and HIP moieties of HIP-CoA, dramatically decreased the affinity of KstR2(Mtb) for HIP-CoA but not for its operator sequence. The variant of R162M that decreased the affinity for HIP-CoA (ΔΔG = 13 kJ mol(-1)) is consistent with the loss of three hydrogen bonds as indicated in the structural data. A 24-bp operator sequence bound two dimers of KstR2. Structural comparisons with a ligand-free rhodococcal homologue and a DNA-bound homologue suggest that HIP-CoA induces conformational changes of the DNA-binding domains of the dimer that preclude their proper positioning in the major groove of DNA. The results provide insight into KstR2-mediated regulation of expression of steroid catabolic genes and the determinants of ligand binding in TFRs.
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Affiliation(s)
- Adam M Crowe
- From the Departments of Biochemistry and Molecular Biology and
| | - Peter J Stogios
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and
| | - Israël Casabon
- Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada, and The Midwest Center for Structural Genomics (MCSG), Argonne National Laboratory, Argonne, Illinois 60439
| | - Lindsay D Eltis
- From the Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver V6T 1Z3, Canada,
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31
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De Majumdar S, Yu J, Spencer J, Tikhonova IG, Schneiders T. Molecular basis of non-mutational derepression of ramA in Klebsiella pneumoniae. J Antimicrob Chemother 2014; 69:2681-9. [PMID: 25140579 DOI: 10.1093/jac/dku203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The ram locus, consisting of the romA-ramA genes, is repressed by the tetracycline-type regulator RamR, where regulation is abolished due to loss-of-function mutations within the protein or ligand interactions. The aim of this study was to determine whether the phenothiazines (chlorpromazine and thioridazine) directly interact with RamR to derepress ramA expression. METHODS Quantitative real-time PCR analyses were performed to determine expression levels of the romA-ramA genes after exposure to the phenothiazines. Electrophoretic mobility shift assays (EMSAs) and in vitro transcription experiments were performed to show direct binding to and repression by RamR. Direct binding of the RamR protein to the phenothiazines was measured by fluorescence spectroscopy experiments and molecular docking models were generated using the RamR crystal structure. RESULTS Exposure to either chlorpromazine or thioridazine resulted in the up-regulation of the romA-ramA genes. EMSAs and in vitro transcription experiments demonstrated that both agents reduce/abolish binding and enhance transcription of the target PI promoter upstream of the ramR-romA genes in Klebsiella pneumoniae compared with RamR alone. Fluorescence spectroscopy measurements demonstrated that RamR directly binds both chlorpromazine and thioridazine with micromolar affinity. Molecular docking analyses using the RamR crystal structure demonstrated that the phenothiazines interact with RamR protein through contacts described for other ligands, in addition to forming unique strong polar interactions at positions D152 and K63. CONCLUSIONS These data demonstrate that phenothiazines can modulate loci linked to the microbe-drug response where RamR is an intracellular target for the phenothiazines, thus resulting in a transient non-mutational derepression of ramA concentrations.
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Affiliation(s)
- Shyamasree De Majumdar
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - Jing Yu
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, Medical Sciences Building, University of Bristol, University Walk, Bristol BS18 1TD, UK
| | - Irina G Tikhonova
- Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Thamarai Schneiders
- Centre for Infection and Immunity, Health Sciences Building, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK
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32
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Black PA, Warren RM, Louw GE, van Helden PD, Victor TC, Kana BD. Energy metabolism and drug efflux in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2014; 58:2491-503. [PMID: 24614376 PMCID: PMC3993223 DOI: 10.1128/aac.02293-13] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The inherent drug susceptibility of microorganisms is determined by multiple factors, including growth state, the rate of drug diffusion into and out of the cell, and the intrinsic vulnerability of drug targets with regard to the corresponding antimicrobial agent. Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant source of global morbidity and mortality, further exacerbated by its ability to readily evolve drug resistance. It is well accepted that drug resistance in M. tuberculosis is driven by the acquisition of chromosomal mutations in genes encoding drug targets/promoter regions; however, a comprehensive description of the molecular mechanisms that fuel drug resistance in the clinical setting is currently lacking. In this context, there is a growing body of evidence suggesting that active extrusion of drugs from the cell is critical for drug tolerance. M. tuberculosis encodes representatives of a diverse range of multidrug transporters, many of which are dependent on the proton motive force (PMF) or the availability of ATP. This suggests that energy metabolism and ATP production through the PMF, which is established by the electron transport chain (ETC), are critical in determining the drug susceptibility of M. tuberculosis. In this review, we detail advances in the study of the mycobacterial ETC and highlight drugs that target various components of the ETC. We provide an overview of some of the efflux pumps present in M. tuberculosis and their association, if any, with drug transport and concomitant effects on drug resistance. The implications of inhibiting drug extrusion, through the use of efflux pump inhibitors, are also discussed.
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Affiliation(s)
- Philippa A. Black
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Gail E. Louw
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Thomas C. Victor
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Bavesh D. Kana
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Radhakrishnan A, Kumar N, Wright CC, Chou TH, Tringides ML, Bolla JR, Lei HT, Rajashankar KR, Su CC, Purdy GE, Yu EW. Crystal structure of the transcriptional regulator Rv0678 of Mycobacterium tuberculosis. J Biol Chem 2014; 289:16526-40. [PMID: 24737322 DOI: 10.1074/jbc.m113.538959] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent work demonstrates that the MmpL (mycobacterial membrane protein large) transporters are dedicated to the export of mycobacterial lipids for cell wall biosynthesis. An MmpL transporter frequently works with an accessory protein, belonging to the MmpS (mycobacterial membrane protein small) family, to transport these key virulence factors. One such efflux system in Mycobacterium tuberculosis is the MmpS5-MmpL5 transporter. The expression of MmpS5-MmpL5 is controlled by the MarR-like transcriptional regulator Rv0678, whose open reading frame is located downstream of the mmpS5-mmpL5 operon. To elucidate the structural basis of Rv0678 regulation, we have determined the crystal structure of this regulator, to 1.64 Å resolution, revealing a dimeric two-domain molecule with an architecture similar to members of the MarR family of transcriptional regulators. Rv0678 is distinct from other MarR regulators in that its DNA-binding and dimerization domains are clustered together. These two domains seemingly cooperate to bind an inducing ligand that we identified as 2-stearoylglycerol, which is a fatty acid glycerol ester. The structure also suggests that the conformational change leading to substrate-mediated derepression is primarily caused by a rigid body rotational motion of the entire DNA-binding domain of the regulator toward the dimerization domain. This movement results in a conformational state that is incompatible with DNA binding. We demonstrate using electrophoretic mobility shift assays that Rv0678 binds to the mmpS5-mmpL5, mmpS4-mmpL4, and the mmpS2-mmpL2 promoters. Binding by Rv0678 was reversed upon the addition of the ligand. These findings provide new insight into the mechanisms of gene regulation in the MarR family of regulators.
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Affiliation(s)
| | | | - Catherine C Wright
- the Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239, and
| | - Tsung-Han Chou
- the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | | | | | | | - Kanagalaghatta R Rajashankar
- the Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439
| | - Chih-Chia Su
- the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011
| | - Georgiana E Purdy
- the Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, Oregon 97239, and
| | - Edward W Yu
- From the Department of Chemistry and the Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011,
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Abstract
The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.
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Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M. The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:379-387. [PMID: 24224534 DOI: 10.1094/mpmi-09-13-0282-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The divergently oriented Sinorhizobium meliloti emrAB (SMc03168 and SMc03167) and emrR (SMc03169) genes are predicted to encode an efflux system of the major facilitator superfamily and a TetR-like transcriptional regulator, respectively. The transcription of the emrA gene was found to be inducible by flavonoids, including luteolin and apigenin, which are known inducers of the nodulation genes in S. meliloti. Interestingly, quercetin, which does not induce nodulation genes, was also a potent inducer of emrA, indicating that NodD is not directly involved in regulation of emrA. The likely regulator of emrAB is EmrR, which binds to palindrome-like sequences in the intergenic region. Several modifications of the palindromes, including an increase of the spacing between the two half sites, prevented binding of EmrR. Binding was also impaired by the presence of luteolin. Mutations in emrA had no obvious effect on symbiosis. This was in contrast to the emrR mutant, which exhibited a symbiotic deficiency with Medicago sativa. Conserved binding sites for TetR-like regulators within the intergenic regions between the emrAB and emrR genes were identified in many symbiotic and pathogenic members of the order Rhizobiales.
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Kumar N, Radhakrishnan A, Wright CC, Chou TH, Lei HT, Bolla JR, Tringides ML, Rajashankar KR, Su CC, Purdy GE, Yu EW. Crystal structure of the transcriptional regulator Rv1219c of Mycobacterium tuberculosis. Protein Sci 2014; 23:423-32. [PMID: 24424575 DOI: 10.1002/pro.2424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 11/07/2022]
Abstract
The Rv1217c-Rv1218c multidrug efflux system, which belongs to the ATP-binding cassette superfamily, recognizes and actively extrudes a variety of structurally unrelated toxic chemicals and mediates the intrinsic resistance to these antimicrobials in Mycobacterium tuberculosis. The expression of Rv1217c-Rv1218c is controlled by the TetR-like transcriptional regulator Rv1219c, which is encoded by a gene immediately upstream of rv1218c. To elucidate the structural basis of Rv1219c regulation, we have determined the crystal structure of Rv1219c, which reveals a dimeric two-domain molecule with an entirely helical architecture similar to members of the TetR family of transcriptional regulators. The N-terminal domains of the Rv1219c dimer are separated by a large center-to-center distance of 64 Å. The C-terminal domain of each protomer possesses a large cavity. Docking of small compounds to Rv1219c suggests that this large cavity forms a multidrug binding pocket, which can accommodate a variety of structurally unrelated antimicrobial agents. The internal wall of the multidrug binding site is surrounded by seven aromatic residues, indicating that drug binding may be governed by aromatic stacking interactions. In addition, fluorescence polarization reveals that Rv1219c binds drugs in the micromolar range.
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Affiliation(s)
- Nitin Kumar
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
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Guo HM, Mao RZ, Wang QT, Niu HY, Xie MS, Qu GR. Pd(II)-Catalyzed One-Pot, Three-Step Route for the Synthesis of Unsymmetrical Acridines. Org Lett 2013; 15:5460-3. [DOI: 10.1021/ol402596g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hai-Ming Guo
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Run-Ze Mao
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qiao-Tian Wang
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Hong-Ying Niu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ming-Sheng Xie
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Gui-Rong Qu
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, Henan, China, and School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
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Yang S, Gao Z, Li T, Yang M, Zhang T, Dong Y, He ZG. Structural basis for interaction between Mycobacterium smegmatis Ms6564, a TetR family master regulator, and its target DNA. J Biol Chem 2013; 288:23687-95. [PMID: 23803605 DOI: 10.1074/jbc.m113.468694] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Master regulators, which broadly affect expression of diverse genes, play critical roles in bacterial growth and environmental adaptation. However, the underlying mechanism by which such regulators interact with their cognate DNA remains to be elucidated. In this study, we solved the crystal structure of a broad regulator Ms6564 in Mycobacterium smegmatis and its protein-operator complex at resolutions of 1.9 and 2.5 Å, respectively. Similar to other typical TetR family regulators, two dimeric Ms6564 molecules were found to bind to opposite sides of target DNA. However, the recognition helix of Ms6564 inserted only slightly into the DNA major groove. Unexpectedly, 11 disordered water molecules bridged the interface of TetR family regulator DNA. Although the DNA was deformed upon Ms6564 binding, it still retained the conformation of B-form DNA. Within the DNA-binding domain of Ms6564, only two amino acids residues directly interacted with the bases of cognate DNA. Lys-47 was found to be essential for the specific DNA binding ability of Ms6564. These data indicate that Ms6564 can bind DNA with strong affinity but makes flexible contacts with DNA. Our study suggests that Ms6564 might slide more easily along the genomic DNA and extensively regulate the expression of diverse genes in M. smegmatis.
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Affiliation(s)
- Shifan Yang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Kim S, Kim KJ. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of Rv2606c from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:578-80. [PMID: 23695582 PMCID: PMC3660906 DOI: 10.1107/s1744309113010683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 04/19/2013] [Indexed: 11/10/2022]
Abstract
Tuberculosis is a widespread and deadly infectious disease, and one third of the human population is already infected. Vitamin B6 is known to be synthesized through consecutive reactions mediated by pyridoxal biosynthesis lyase (PdxS) and glutamine amidotransferase (PdxT). The gene product Rv2606c, the PdxS pyridoxal biosynthesis lyase from Mycobacterium tuberculosis, was crystallized using the hanging-drop vapour-diffusion method in the presence of 8%(w/v) PEG 8000, 0.1 M 3-(cyclohexylamino)-1-propanesulfonic acid pH 10.5 and 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 1.7 Å on a synchrotron beamline. The crystal belonged to space group I222 or I212121, with unit-cell parameters a = 110.75, b = 126.08, c = 180.82 Å, α = β = γ = 90°. With three molecules per asymmetric unit, the crystal volume per unit protein weight (VM) was 3.79 Å(3) Da(-1).
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Affiliation(s)
- Sangwoo Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Republic of Korea
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40
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Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase. Biochem Biophys Res Commun 2013; 435:255-9. [PMID: 23643787 DOI: 10.1016/j.bbrc.2013.04.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022]
Abstract
Tuberculosis is a lethal infectious disease caused by Mycobacterium tuberculosis. We determined the crystal structure of Rv2606c, a potential pyridoxal biosynthesis lyase (PdxS), from M. tuberculosis H37Rv at 1.8 Å resolution. The overall structure of the protein, composed of a (β/α)8-barrel and two small 310-helices, was quite similar to those of other PdxS proteins. A glycerol molecule was observed to be bound at the active site of the Rv2606c structure through interactions with the conserved residues of Asp29 and Lys86, providing information regarding the potential active site and the substrate-binding environment of the protein. The interface for Rv2606c dodecamerization, which is primarily mediated by salt bridges and hydrophobic interactions, was quite different from those of other PdxS proteins. Furthermore, we observed that the Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as PdxS and PdxT in M. tuberculosis.
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